Motion of the hydrogen bond proton in cytosine and the transition between its normal and imino states

The electronic structure of an infinite poly-guanine - poly-cytosine DNA molecule in its dry A-helix structure is studied by means of density-functional calculations. An extensive study of 30 nucleic base pairs is performed to validate the method. The electronic energy bands of DNA close to the Fermi level are then analyzed in order to clarify the electron transport properties in this particularly simple DNA realization, probably the best suited candidate for conduction. The ...

We have investigated the impact of microsolvation on the shape resonance states of nucleobases, taking cytosine as a case study. To characterize the resonance position and decay width of the metastable states, we employed the newly developed DLPNO-based EA-EOMCCSD method in conjunction with resonance via Pad\'e approximation. Our calculations show that the presence of water molecules causes a red shift in the resonance position and an increase in the lifetime for all three re...

We are presenting the electronic photo fragment spectra of the protonated pyrimidine DNA bases homo-dimers. Only the thymine dimer exhibits a well structured vibrational progression, while protonated monomer shows broad vibrational bands. This shows that proton bonding can block some non radiative processes present in the monomer.

We report ab initio excited-state dynamics simulations on isolated thymine to investigate the mechanism of intersystem crossing, based on CASSCF potential energy surfaces and the \textsc{Sharc} surface hopping method. We show that even though $S_2 \rightarrow S_1$ internal conversion is not described accurately with CASSCF, intersystem crossing can be correctly simulated. Intersystem crossing in thymine occurs from the $S_1$ ($^1n\pi^*$) minimum, via a nearby crossing with $T...

The hydrogen bond is usually described within the clamped nucleus approximation in which electronic and vibrational motions are considered separately. This approach leads to a double-well potential which facilitates proton tunnelling. In this work, the hydrogen bond is described by a formalism based on the non-adiabatic Hamiltonian in which electronic and vibrational motions are coupled. Quasi-degeneracy associated with the hydrogen bond supports this approach which is shown ...

Hybrid QM(DFT)/MM molecular dynamics simulations have been carried out for the Watson-Crick base pair of 9-ethyl-8-phenyladenine and 1-cyclohexyluracil in deuterochloroform solution at room temperature. Trajectories are analyzed putting special attention to the geometric correlations of the $\NHN$ and $\NHO$ hydrogen bonds in the base pair. Further, based on empirical correlations between the hydrogen bond bond length and the fundamental NH stretching frequency its fluctuat...

We report a biased QM/MM molecular dynamics study of the dissociation process of cytidine-cytidine complexes mediated by Ag+ or H+ ions. We performed calculations under real solvent conditions and obtained the free energy profiles (FEP) by thermodynamic integration technique to give deep insights on the dissociation process. For all geometries corresponding to key points on FEP the noncovalent interaction descriptors (NCI) were calculated and the details of dissociation mecha...

Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the dominant collective motions to correspond to a tensile 'opening' mode and two shear 'sliding' and 'tearing' modes in the orthogonal plane. The stacking interactio...

The interaction of heavy charged particles with DNA is of interest for several areas, from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried out. Ehrenfest dynamics was used to study the evolution of the system during and after the proton impact up to about 193 fs. This time was long enough to observe the dissociation of the target, which occurs between 80-100 fs. The effect of b...

DNA has been proposed as a chemical platform for computing and data storage, paving the way for building DNA-based computers. Recently, DNA has been hypothesized as an ideal quantum computer with the base pairs working as Josephson junctions. There are still major challenges to be overcome in these directions, but they do not prevent deviceful perspectives of the main problem. The present paper explores DNA base pairs as elementary units for a scalable nuclear magnetic resona...